rs10400305

chr11-57381258-G-Achr11-57381258-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.748 in 152,362 control chromosomes in the GnomAD database, including 45,103 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.75 (45023 hom., cov: 32)
  • Exomes 𝑓: 0.87 (80 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113721 AN: 152028 Hom.: 45010 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.780

GnomAD4 exome AF: 0.866 AC: 187 AN: 216 Hom.: 80 AF XY: 0.855 AC XY: 142 AN XY: 166

Gnomad4 AFR exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.851

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.748 AC: 113770 AN: 152146 Hom.: 45023 Cov.: 32 AF XY: 0.757 AC XY: 56336 AN XY: 74416

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.782

Alfa AF: 0.832 Hom.: 104018

Bravo AF: 0.734

Asia WGS AF: 0.903 AC: 3138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.2
Dann	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10400305; hg19: chr11-57148731;